data_2DPU # _entry.id 2DPU # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.351 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 2DPU pdb_00002dpu 10.2210/pdb2dpu/pdb NDB PD0809 ? ? RCSB RCSB025700 ? ? WWPDB D_1000025700 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1BM9 'This is the wild-type apo-structure' unspecified PDB 1J0R 'This is the apo-structure of the mutant RTP.C110S' unspecified PDB 1F4K 'This is the same structure solved in a different space group' unspecified PDB 2DPD 'This is the same structure solved in a different space group' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2DPU _pdbx_database_status.recvd_initial_deposition_date 2006-05-15 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Vivian, J.P.' 1 'Wilce, J.' 2 'Wilce, M.C.J.' 3 # _citation.id primary _citation.title 'Crystal structure of the replication termination protein in complex with a pseudosymmetric 21mer B-site DNA' _citation.journal_abbrev 'to be published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Vivian, J.P.' 1 ? primary 'Wilce, J.' 2 ? primary 'Wilce, M.C.J.' 3 ? # _cell.entry_id 2DPU _cell.length_a 73.049 _cell.length_b 73.049 _cell.length_c 68.411 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 2DPU _symmetry.space_group_name_H-M 'P 62' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 171 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-D(P*AP*TP*GP*TP*TP*CP*AP*TP*AP*G)-3'" 3059.028 1 ? ? ? ? 2 polymer syn "5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*T)-3'" 3332.210 1 ? ? ? ? 3 polymer man 'Replication termination protein' 14531.099 1 ? C110S ? ? 4 water nat water 18.015 8 ? ? ? ? # _entity_name_com.entity_id 3 _entity_name_com.name 'Replication terminator protein' # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no no '(DA)(DT)(DG)(DT)(DT)(DC)(DA)(DT)(DA)(DG)' ATGTTCATAG D ? 2 polydeoxyribonucleotide no no '(DC)(DT)(DA)(DT)(DG)(DA)(DA)(DC)(DA)(DT)(DT)' CTATGAACATT E ? 3 'polypeptide(L)' no no ;MKEEKRSSTGFLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEGA KLQEVVLYQFKDYEAAKLYKKQLKVELDRSKKLIEKALSDNF ; ;MKEEKRSSTGFLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEGA KLQEVVLYQFKDYEAAKLYKKQLKVELDRSKKLIEKALSDNF ; A ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DA n 1 2 DT n 1 3 DG n 1 4 DT n 1 5 DT n 1 6 DC n 1 7 DA n 1 8 DT n 1 9 DA n 1 10 DG n 2 1 DC n 2 2 DT n 2 3 DA n 2 4 DT n 2 5 DG n 2 6 DA n 2 7 DA n 2 8 DC n 2 9 DA n 2 10 DT n 2 11 DT n 3 1 MET n 3 2 LYS n 3 3 GLU n 3 4 GLU n 3 5 LYS n 3 6 ARG n 3 7 SER n 3 8 SER n 3 9 THR n 3 10 GLY n 3 11 PHE n 3 12 LEU n 3 13 VAL n 3 14 LYS n 3 15 GLN n 3 16 ARG n 3 17 ALA n 3 18 PHE n 3 19 LEU n 3 20 LYS n 3 21 LEU n 3 22 TYR n 3 23 MET n 3 24 ILE n 3 25 THR n 3 26 MET n 3 27 THR n 3 28 GLU n 3 29 GLN n 3 30 GLU n 3 31 ARG n 3 32 LEU n 3 33 TYR n 3 34 GLY n 3 35 LEU n 3 36 LYS n 3 37 LEU n 3 38 LEU n 3 39 GLU n 3 40 VAL n 3 41 LEU n 3 42 ARG n 3 43 SER n 3 44 GLU n 3 45 PHE n 3 46 LYS n 3 47 GLU n 3 48 ILE n 3 49 GLY n 3 50 PHE n 3 51 LYS n 3 52 PRO n 3 53 ASN n 3 54 HIS n 3 55 THR n 3 56 GLU n 3 57 VAL n 3 58 TYR n 3 59 ARG n 3 60 SER n 3 61 LEU n 3 62 HIS n 3 63 GLU n 3 64 LEU n 3 65 LEU n 3 66 ASP n 3 67 ASP n 3 68 GLY n 3 69 ILE n 3 70 LEU n 3 71 LYS n 3 72 GLN n 3 73 ILE n 3 74 LYS n 3 75 VAL n 3 76 LYS n 3 77 LYS n 3 78 GLU n 3 79 GLY n 3 80 ALA n 3 81 LYS n 3 82 LEU n 3 83 GLN n 3 84 GLU n 3 85 VAL n 3 86 VAL n 3 87 LEU n 3 88 TYR n 3 89 GLN n 3 90 PHE n 3 91 LYS n 3 92 ASP n 3 93 TYR n 3 94 GLU n 3 95 ALA n 3 96 ALA n 3 97 LYS n 3 98 LEU n 3 99 TYR n 3 100 LYS n 3 101 LYS n 3 102 GLN n 3 103 LEU n 3 104 LYS n 3 105 VAL n 3 106 GLU n 3 107 LEU n 3 108 ASP n 3 109 ARG n 3 110 SER n 3 111 LYS n 3 112 LYS n 3 113 LEU n 3 114 ILE n 3 115 GLU n 3 116 LYS n 3 117 ALA n 3 118 LEU n 3 119 SER n 3 120 ASP n 3 121 ASN n 3 122 PHE n # _entity_src_gen.entity_id 3 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus Bacillus _entity_src_gen.pdbx_gene_src_gene rtp _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Bacillus subtilis' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 1423 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus Escherichia _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain BL21.pLysS _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name pET-3 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_isoform 1 UNP RTP_BACSU P68732 3 ;MKEEKRSSTGFLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEGA KLQEVVLYQFKDYEAAKLYKKQLKVELDRCKKLIEKALSDNF ; 8 ? 2 PDB 2DPU 2DPU 1 ? ? ? 3 PDB 2DPU 2DPU 2 ? ? ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 2DPU A 1 ? 122 ? P68732 8 ? 129 ? 1 122 2 2 2DPU D 1 ? 10 ? 2DPU 12 ? 21 ? 12 21 3 3 2DPU E 1 ? 11 ? 2DPU 1 ? 11 ? 1 11 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 2DPU _struct_ref_seq_dif.mon_id SER _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 110 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code P68732 _struct_ref_seq_dif.db_mon_id CYS _struct_ref_seq_dif.pdbx_seq_db_seq_num 117 _struct_ref_seq_dif.details 'engineered mutation' _struct_ref_seq_dif.pdbx_auth_seq_num 110 _struct_ref_seq_dif.pdbx_ordinal 1 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 2DPU _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.49 _exptl_crystal.density_percent_sol 50.67 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 4.6 _exptl_crystal_grow.pdbx_details '1.75M ammonium sulfate, 0.1M sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 'ammonium sulfate' ? ? ? 1 2 1 'sodium acetate' ? ? ? 1 3 1 HOH ? ? ? 1 4 2 'ammonium sulfate' ? ? ? 1 5 2 'sodium acetate' ? ? ? 1 6 2 HOH ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'MAR scanner 345 mm plate' _diffrn_detector.pdbx_collection_date 2000-06-05 _diffrn_detector.details mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator mirrors _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 2DPU _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 40 _reflns.d_resolution_high 3.1 _reflns.number_obs 3807 _reflns.number_all 3829 _reflns.percent_possible_obs 99.5 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate 63 _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 3.10 _reflns_shell.d_res_low 3.18 _reflns_shell.percent_possible_all 98.9 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 2DPU _refine.ls_number_reflns_obs 3636 _refine.ls_number_reflns_all 3807 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 40 _refine.ls_d_res_high 3.10 _refine.ls_percent_reflns_obs 99.50 _refine.ls_R_factor_obs 0.2061 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.20199 _refine.ls_R_factor_R_free 0.30609 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.5 _refine.ls_number_reflns_R_free 170 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc .961 _refine.correlation_coeff_Fo_to_Fc_free .885 _refine.B_iso_mean 50.068 _refine.aniso_B[1][1] -3.47 _refine.aniso_B[2][2] -3.47 _refine.aniso_B[3][3] 5.20 _refine.aniso_B[1][2] -1.73 _refine.aniso_B[1][3] .00 _refine.aniso_B[2][3] .00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii .80 _refine.pdbx_solvent_shrinkage_radii .80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free .597 _refine.overall_SU_ML .505 _refine.overall_SU_B 72.990 _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 961 _refine_hist.pdbx_number_atoms_nucleic_acid 427 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 8 _refine_hist.number_atoms_total 1396 _refine_hist.d_res_high 3.10 _refine_hist.d_res_low 40 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d .008 .022 ? 1446 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.369 2.364 ? 2025 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 4.115 5.000 ? 114 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 42.371 24.545 ? 44 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 20.320 15.000 ? 209 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 14.308 15.000 ? 5 'X-RAY DIFFRACTION' ? r_chiral_restr .059 .200 ? 228 'X-RAY DIFFRACTION' ? r_gen_planes_refined .003 .020 ? 899 'X-RAY DIFFRACTION' ? r_nbd_refined .219 .200 ? 658 'X-RAY DIFFRACTION' ? r_nbtor_refined .304 .200 ? 925 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined .142 .200 ? 56 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined .237 .200 ? 69 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined .130 .200 ? 8 'X-RAY DIFFRACTION' ? r_mcbond_it .304 1.500 ? 586 'X-RAY DIFFRACTION' ? r_mcangle_it .572 2.000 ? 916 'X-RAY DIFFRACTION' ? r_scbond_it .720 3.000 ? 1085 'X-RAY DIFFRACTION' ? r_scangle_it 1.314 4.500 ? 1109 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 3.101 _refine_ls_shell.d_res_low 3.182 _refine_ls_shell.number_reflns_R_work 258 _refine_ls_shell.R_factor_R_work 0.289 _refine_ls_shell.percent_reflns_obs 98.90 _refine_ls_shell.R_factor_R_free 0.472 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 11 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 2DPU _struct.title 'Crystal structure of the replication termination protein in complex with a pseudosymmetric 21mer B-site DNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2DPU _struct_keywords.pdbx_keywords 'DNA BINDING PROTEIN/DNA' _struct_keywords.text 'protein-DNA complex, winged-helix, DNA replication, DNA BINDING PROTEIN-DNA COMPLEX' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 4 ? F N N 4 ? # _struct_biol.id 1 _struct_biol.details ;The asymmetric unit contains a monomer. The biological dimer is generated by the operation: rotation: -1 0 0 0-1 0 0 0 1 translation: 1 1 0 ; # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 LYS C 14 ? GLU C 28 ? LYS A 14 GLU A 28 1 ? 15 HELX_P HELX_P2 2 TYR C 33 ? PHE C 45 ? TYR A 33 PHE A 45 1 ? 13 HELX_P HELX_P3 3 ASN C 53 ? ASP C 67 ? ASN A 53 ASP A 67 1 ? 15 HELX_P HELX_P4 4 ASP C 92 ? LYS C 100 ? ASP A 92 LYS A 100 1 ? 9 HELX_P HELX_P5 5 LEU C 103 ? ASN C 121 ? LEU A 103 ASN A 121 1 ? 19 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A DA 1 N1 ? ? ? 1_555 B DT 10 N3 ? ? D DA 12 E DT 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DA 1 N6 ? ? ? 1_555 B DT 10 O4 ? ? D DA 12 E DT 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DT 2 N3 ? ? ? 1_555 B DA 9 N1 ? ? D DT 13 E DA 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DT 2 O4 ? ? ? 1_555 B DA 9 N6 ? ? D DT 13 E DA 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 8 N3 ? ? D DG 14 E DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 8 O2 ? ? D DG 14 E DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 8 N4 ? ? D DG 14 E DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 7 N1 ? ? D DT 15 E DA 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 7 N6 ? ? D DT 15 E DA 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B DA 6 N1 ? ? D DT 16 E DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 5 O4 ? ? ? 1_555 B DA 6 N6 ? ? D DT 16 E DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 6 O2 ? ? ? 1_555 B DG 5 N2 ? ? D DC 17 E DG 5 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog13 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? D DA 18 E DT 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? D DA 18 E DT 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 3 N1 ? ? D DT 19 E DA 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 3 N6 ? ? D DT 19 E DA 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 9 N1 ? ? ? 1_555 B DT 2 N3 ? ? D DA 20 E DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DA 9 N6 ? ? ? 1_555 B DT 2 O4 ? ? D DA 20 E DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 1 N3 ? ? D DG 21 E DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 1 O2 ? ? D DG 21 E DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 1 N4 ? ? D DG 21 E DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 2 _struct_sheet.details ? # _struct_sheet_order.sheet_id A _struct_sheet_order.range_id_1 1 _struct_sheet_order.range_id_2 2 _struct_sheet_order.offset ? _struct_sheet_order.sense anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 LEU C 70 ? LYS C 74 ? LEU A 70 LYS A 74 A 2 VAL C 86 ? PHE C 90 ? VAL A 86 PHE A 90 # _pdbx_struct_sheet_hbond.sheet_id A _pdbx_struct_sheet_hbond.range_id_1 1 _pdbx_struct_sheet_hbond.range_id_2 2 _pdbx_struct_sheet_hbond.range_1_label_atom_id N _pdbx_struct_sheet_hbond.range_1_label_comp_id LYS _pdbx_struct_sheet_hbond.range_1_label_asym_id C _pdbx_struct_sheet_hbond.range_1_label_seq_id 71 _pdbx_struct_sheet_hbond.range_1_PDB_ins_code ? _pdbx_struct_sheet_hbond.range_1_auth_atom_id N _pdbx_struct_sheet_hbond.range_1_auth_comp_id LYS _pdbx_struct_sheet_hbond.range_1_auth_asym_id A _pdbx_struct_sheet_hbond.range_1_auth_seq_id 71 _pdbx_struct_sheet_hbond.range_2_label_atom_id O _pdbx_struct_sheet_hbond.range_2_label_comp_id GLN _pdbx_struct_sheet_hbond.range_2_label_asym_id C _pdbx_struct_sheet_hbond.range_2_label_seq_id 89 _pdbx_struct_sheet_hbond.range_2_PDB_ins_code ? _pdbx_struct_sheet_hbond.range_2_auth_atom_id O _pdbx_struct_sheet_hbond.range_2_auth_comp_id GLN _pdbx_struct_sheet_hbond.range_2_auth_asym_id A _pdbx_struct_sheet_hbond.range_2_auth_seq_id 89 # _database_PDB_matrix.entry_id 2DPU _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 2DPU _atom_sites.fract_transf_matrix[1][1] 0.013689 _atom_sites.fract_transf_matrix[1][2] 0.007904 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.015807 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.014618 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DA 1 12 12 DA A D . n A 1 2 DT 2 13 13 DT T D . n A 1 3 DG 3 14 14 DG G D . n A 1 4 DT 4 15 15 DT T D . n A 1 5 DT 5 16 16 DT T D . n A 1 6 DC 6 17 17 DC C D . n A 1 7 DA 7 18 18 DA A D . n A 1 8 DT 8 19 19 DT T D . n A 1 9 DA 9 20 20 DA A D . n A 1 10 DG 10 21 21 DG G D . n B 2 1 DC 1 1 1 DC C E . n B 2 2 DT 2 2 2 DT T E . n B 2 3 DA 3 3 3 DA A E . n B 2 4 DT 4 4 4 DT T E . n B 2 5 DG 5 5 5 DG G E . n B 2 6 DA 6 6 6 DA A E . n B 2 7 DA 7 7 7 DA A E . n B 2 8 DC 8 8 8 DC C E . n B 2 9 DA 9 9 9 DA A E . n B 2 10 DT 10 10 10 DT T E . n B 2 11 DT 11 11 11 DT T E . n C 3 1 MET 1 1 ? ? ? A . n C 3 2 LYS 2 2 ? ? ? A . n C 3 3 GLU 3 3 ? ? ? A . n C 3 4 GLU 4 4 ? ? ? A . n C 3 5 LYS 5 5 ? ? ? A . n C 3 6 ARG 6 6 ? ? ? A . n C 3 7 SER 7 7 ? ? ? A . n C 3 8 SER 8 8 8 SER SER A . n C 3 9 THR 9 9 9 THR THR A . n C 3 10 GLY 10 10 10 GLY GLY A . n C 3 11 PHE 11 11 11 PHE PHE A . n C 3 12 LEU 12 12 12 LEU LEU A . n C 3 13 VAL 13 13 13 VAL VAL A . n C 3 14 LYS 14 14 14 LYS LYS A . n C 3 15 GLN 15 15 15 GLN GLN A . n C 3 16 ARG 16 16 16 ARG ARG A . n C 3 17 ALA 17 17 17 ALA ALA A . n C 3 18 PHE 18 18 18 PHE PHE A . n C 3 19 LEU 19 19 19 LEU LEU A . n C 3 20 LYS 20 20 20 LYS LYS A . n C 3 21 LEU 21 21 21 LEU LEU A . n C 3 22 TYR 22 22 22 TYR TYR A . n C 3 23 MET 23 23 23 MET MET A . n C 3 24 ILE 24 24 24 ILE ILE A . n C 3 25 THR 25 25 25 THR THR A . n C 3 26 MET 26 26 26 MET MET A . n C 3 27 THR 27 27 27 THR THR A . n C 3 28 GLU 28 28 28 GLU GLU A . n C 3 29 GLN 29 29 29 GLN GLN A . n C 3 30 GLU 30 30 30 GLU GLU A . n C 3 31 ARG 31 31 31 ARG ARG A . n C 3 32 LEU 32 32 32 LEU LEU A . n C 3 33 TYR 33 33 33 TYR TYR A . n C 3 34 GLY 34 34 34 GLY GLY A . n C 3 35 LEU 35 35 35 LEU LEU A . n C 3 36 LYS 36 36 36 LYS LYS A . n C 3 37 LEU 37 37 37 LEU LEU A . n C 3 38 LEU 38 38 38 LEU LEU A . n C 3 39 GLU 39 39 39 GLU GLU A . n C 3 40 VAL 40 40 40 VAL VAL A . n C 3 41 LEU 41 41 41 LEU LEU A . n C 3 42 ARG 42 42 42 ARG ARG A . n C 3 43 SER 43 43 43 SER SER A . n C 3 44 GLU 44 44 44 GLU GLU A . n C 3 45 PHE 45 45 45 PHE PHE A . n C 3 46 LYS 46 46 46 LYS LYS A . n C 3 47 GLU 47 47 47 GLU GLU A . n C 3 48 ILE 48 48 48 ILE ILE A . n C 3 49 GLY 49 49 49 GLY GLY A . n C 3 50 PHE 50 50 50 PHE PHE A . n C 3 51 LYS 51 51 51 LYS LYS A . n C 3 52 PRO 52 52 52 PRO PRO A . n C 3 53 ASN 53 53 53 ASN ASN A . n C 3 54 HIS 54 54 54 HIS HIS A . n C 3 55 THR 55 55 55 THR THR A . n C 3 56 GLU 56 56 56 GLU GLU A . n C 3 57 VAL 57 57 57 VAL VAL A . n C 3 58 TYR 58 58 58 TYR TYR A . n C 3 59 ARG 59 59 59 ARG ARG A . n C 3 60 SER 60 60 60 SER SER A . n C 3 61 LEU 61 61 61 LEU LEU A . n C 3 62 HIS 62 62 62 HIS HIS A . n C 3 63 GLU 63 63 63 GLU GLU A . n C 3 64 LEU 64 64 64 LEU LEU A . n C 3 65 LEU 65 65 65 LEU LEU A . n C 3 66 ASP 66 66 66 ASP ASP A . n C 3 67 ASP 67 67 67 ASP ASP A . n C 3 68 GLY 68 68 68 GLY GLY A . n C 3 69 ILE 69 69 69 ILE ILE A . n C 3 70 LEU 70 70 70 LEU LEU A . n C 3 71 LYS 71 71 71 LYS LYS A . n C 3 72 GLN 72 72 72 GLN GLN A . n C 3 73 ILE 73 73 73 ILE ILE A . n C 3 74 LYS 74 74 74 LYS LYS A . n C 3 75 VAL 75 75 75 VAL VAL A . n C 3 76 LYS 76 76 76 LYS LYS A . n C 3 77 LYS 77 77 77 LYS LYS A . n C 3 78 GLU 78 78 78 GLU GLU A . n C 3 79 GLY 79 79 79 GLY GLY A . n C 3 80 ALA 80 80 80 ALA ALA A . n C 3 81 LYS 81 81 81 LYS LYS A . n C 3 82 LEU 82 82 82 LEU LEU A . n C 3 83 GLN 83 83 83 GLN GLN A . n C 3 84 GLU 84 84 84 GLU GLU A . n C 3 85 VAL 85 85 85 VAL VAL A . n C 3 86 VAL 86 86 86 VAL VAL A . n C 3 87 LEU 87 87 87 LEU LEU A . n C 3 88 TYR 88 88 88 TYR TYR A . n C 3 89 GLN 89 89 89 GLN GLN A . n C 3 90 PHE 90 90 90 PHE PHE A . n C 3 91 LYS 91 91 91 LYS LYS A . n C 3 92 ASP 92 92 92 ASP ASP A . n C 3 93 TYR 93 93 93 TYR TYR A . n C 3 94 GLU 94 94 94 GLU GLU A . n C 3 95 ALA 95 95 95 ALA ALA A . n C 3 96 ALA 96 96 96 ALA ALA A . n C 3 97 LYS 97 97 97 LYS LYS A . n C 3 98 LEU 98 98 98 LEU LEU A . n C 3 99 TYR 99 99 99 TYR TYR A . n C 3 100 LYS 100 100 100 LYS LYS A . n C 3 101 LYS 101 101 101 LYS LYS A . n C 3 102 GLN 102 102 102 GLN GLN A . n C 3 103 LEU 103 103 103 LEU LEU A . n C 3 104 LYS 104 104 104 LYS LYS A . n C 3 105 VAL 105 105 105 VAL VAL A . n C 3 106 GLU 106 106 106 GLU GLU A . n C 3 107 LEU 107 107 107 LEU LEU A . n C 3 108 ASP 108 108 108 ASP ASP A . n C 3 109 ARG 109 109 109 ARG ARG A . n C 3 110 SER 110 110 110 SER SER A . n C 3 111 LYS 111 111 111 LYS LYS A . n C 3 112 LYS 112 112 112 LYS LYS A . n C 3 113 LEU 113 113 113 LEU LEU A . n C 3 114 ILE 114 114 114 ILE ILE A . n C 3 115 GLU 115 115 115 GLU GLU A . n C 3 116 LYS 116 116 116 LYS LYS A . n C 3 117 ALA 117 117 117 ALA ALA A . n C 3 118 LEU 118 118 118 LEU LEU A . n C 3 119 SER 119 119 119 SER SER A . n C 3 120 ASP 120 120 120 ASP ASP A . n C 3 121 ASN 121 121 121 ASN ASN A . n C 3 122 PHE 122 122 122 PHE PHE A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code D 4 HOH 1 1 1 HOH HOH D . E 4 HOH 1 12 2 HOH HOH E . E 4 HOH 2 13 3 HOH HOH E . E 4 HOH 3 14 6 HOH HOH E . F 4 HOH 1 123 4 HOH HOH A . F 4 HOH 2 124 5 HOH HOH A . F 4 HOH 3 125 7 HOH HOH A . F 4 HOH 4 126 8 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 4_665 -x+1,-y+1,z -1.0000000000 0.0000000000 0.0000000000 36.5245000000 0.0000000000 -1.0000000000 0.0000000000 63.2622897210 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2007-05-15 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-11 5 'Structure model' 1 4 2021-11-10 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Refinement description' 4 5 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' software 2 5 'Structure model' database_2 3 5 'Structure model' struct_ref_seq_dif # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_software.classification' 2 4 'Structure model' '_software.name' 3 5 'Structure model' '_database_2.pdbx_DOI' 4 5 'Structure model' '_database_2.pdbx_database_accession' 5 5 'Structure model' '_struct_ref_seq_dif.details' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.2.0005 ? 1 MAR345 'data collection' 345 ? 2 DENZO 'data reduction' . ? 3 SCALEPACK 'data scaling' . ? 4 MOLREP phasing . ? 5 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O A ILE 69 ? ? CB A LYS 91 ? ? 1.78 2 1 O A ILE 69 ? ? N A LYS 91 ? ? 2.09 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" D DT 13 ? ? "C1'" D DT 13 ? ? N1 D DT 13 ? ? 111.86 108.30 3.56 0.30 N 2 1 "O4'" D DT 15 ? ? "C1'" D DT 15 ? ? N1 D DT 15 ? ? 110.49 108.30 2.19 0.30 N 3 1 "O4'" D DA 20 ? ? "C1'" D DA 20 ? ? N9 D DA 20 ? ? 110.91 108.30 2.61 0.30 N 4 1 "O4'" E DC 1 ? ? "C1'" E DC 1 ? ? N1 E DC 1 ? ? 113.14 108.30 4.84 0.30 N 5 1 "C3'" E DT 10 ? ? "O3'" E DT 10 ? ? P E DT 11 ? ? 128.07 119.70 8.37 1.20 Y 6 1 "O4'" E DT 11 ? ? "C1'" E DT 11 ? ? N1 E DT 11 ? ? 110.81 108.30 2.51 0.30 N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 PHE A 11 ? ? -77.40 -115.75 2 1 GLN A 29 ? ? -144.16 -65.43 3 1 ARG A 31 ? ? 55.01 81.50 4 1 ILE A 69 ? ? -128.59 -104.70 5 1 ILE A 73 ? ? 162.77 70.41 6 1 GLU A 84 ? ? -103.60 50.45 7 1 LYS A 91 ? ? -93.18 -62.71 8 1 LYS A 100 ? ? -66.47 19.92 9 1 LYS A 101 ? ? -136.11 -43.71 10 1 GLN A 102 ? ? -67.16 3.00 # _pdbx_validate_peptide_omega.id 1 _pdbx_validate_peptide_omega.PDB_model_num 1 _pdbx_validate_peptide_omega.auth_comp_id_1 GLN _pdbx_validate_peptide_omega.auth_asym_id_1 A _pdbx_validate_peptide_omega.auth_seq_id_1 72 _pdbx_validate_peptide_omega.PDB_ins_code_1 ? _pdbx_validate_peptide_omega.label_alt_id_1 ? _pdbx_validate_peptide_omega.auth_comp_id_2 ILE _pdbx_validate_peptide_omega.auth_asym_id_2 A _pdbx_validate_peptide_omega.auth_seq_id_2 73 _pdbx_validate_peptide_omega.PDB_ins_code_2 ? _pdbx_validate_peptide_omega.label_alt_id_2 ? _pdbx_validate_peptide_omega.omega -144.48 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A MET 1 ? C MET 1 2 1 Y 1 A LYS 2 ? C LYS 2 3 1 Y 1 A GLU 3 ? C GLU 3 4 1 Y 1 A GLU 4 ? C GLU 4 5 1 Y 1 A LYS 5 ? C LYS 5 6 1 Y 1 A ARG 6 ? C ARG 6 7 1 Y 1 A SER 7 ? C SER 7 # _ndb_struct_conf_na.entry_id 2DPU _ndb_struct_conf_na.feature 'b-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DA 1 1_555 B DT 10 1_555 -0.612 -0.079 0.202 0.268 -11.898 7.301 1 D_DA12:DT10_E D 12 ? E 10 ? 20 1 1 A DT 2 1_555 B DA 9 1_555 0.894 -0.323 -0.034 3.915 -4.469 -5.624 2 D_DT13:DA9_E D 13 ? E 9 ? 20 1 1 A DG 3 1_555 B DC 8 1_555 -0.087 -0.130 0.205 0.622 -15.960 -5.156 3 D_DG14:DC8_E D 14 ? E 8 ? 19 1 1 A DT 4 1_555 B DA 7 1_555 -0.452 -0.104 -0.165 -3.486 -6.259 -4.667 4 D_DT15:DA7_E D 15 ? E 7 ? 20 1 1 A DT 5 1_555 B DA 6 1_555 -0.219 -0.219 0.074 -8.993 -8.806 -8.250 5 D_DT16:DA6_E D 16 ? E 6 ? 20 1 1 A DC 6 1_555 B DG 5 1_555 -0.319 0.278 -0.064 1.897 -9.064 11.261 6 D_DC17:DG5_E D 17 ? E 5 ? ? 1 1 A DA 7 1_555 B DT 4 1_555 0.451 -0.269 -0.010 -2.677 1.542 -0.196 7 D_DA18:DT4_E D 18 ? E 4 ? 20 1 1 A DT 8 1_555 B DA 3 1_555 0.332 -0.214 -0.316 11.421 2.219 1.747 8 D_DT19:DA3_E D 19 ? E 3 ? 20 1 1 A DA 9 1_555 B DT 2 1_555 -0.351 -0.464 -0.470 -1.405 2.383 -7.190 9 D_DA20:DT2_E D 20 ? E 2 ? 20 1 1 A DG 10 1_555 B DC 1 1_555 0.939 -0.190 -0.137 18.308 0.655 -1.483 10 D_DG21:DC1_E D 21 ? E 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DA 1 1_555 B DT 10 1_555 A DT 2 1_555 B DA 9 1_555 0.171 -0.321 3.174 0.824 0.087 38.322 -0.500 -0.161 3.176 0.132 -1.256 38.330 1 DD_DA12DT13:DA9DT10_EE D 12 ? E 10 ? D 13 ? E 9 ? 1 A DT 2 1_555 B DA 9 1_555 A DG 3 1_555 B DC 8 1_555 -0.468 -0.865 3.208 -2.966 3.528 29.494 -2.393 0.309 3.117 6.877 5.782 29.845 2 DD_DT13DG14:DC8DA9_EE D 13 ? E 9 ? D 14 ? E 8 ? 1 A DG 3 1_555 B DC 8 1_555 A DT 4 1_555 B DA 7 1_555 -0.597 -0.742 3.471 4.041 -4.795 33.936 -0.458 1.676 3.449 -8.129 -6.851 34.493 3 DD_DG14DT15:DA7DC8_EE D 14 ? E 8 ? D 15 ? E 7 ? 1 A DT 4 1_555 B DA 7 1_555 A DT 5 1_555 B DA 6 1_555 0.386 -0.530 3.346 -1.301 -0.444 38.761 -0.743 -0.743 3.338 -0.669 1.959 38.785 4 DD_DT15DT16:DA6DA7_EE D 15 ? E 7 ? D 16 ? E 6 ? 1 A DT 5 1_555 B DA 6 1_555 A DC 6 1_555 B DG 5 1_555 0.713 -0.423 2.907 0.276 -1.188 34.304 -0.552 -1.170 2.925 -2.013 -0.467 34.325 5 DD_DT16DC17:DG5DA6_EE D 16 ? E 6 ? D 17 ? E 5 ? 1 A DC 6 1_555 B DG 5 1_555 A DA 7 1_555 B DT 4 1_555 -1.390 -0.593 3.288 -4.057 6.747 37.494 -1.762 1.604 3.264 10.356 6.228 38.282 6 DD_DC17DA18:DT4DG5_EE D 17 ? E 5 ? D 18 ? E 4 ? 1 A DA 7 1_555 B DT 4 1_555 A DT 8 1_555 B DA 3 1_555 -0.357 -0.540 3.014 -0.540 0.872 29.087 -1.250 0.601 3.003 1.735 1.075 29.104 7 DD_DA18DT19:DA3DT4_EE D 18 ? E 4 ? D 19 ? E 3 ? 1 A DT 8 1_555 B DA 3 1_555 A DA 9 1_555 B DT 2 1_555 -0.454 -1.136 3.612 -1.206 8.100 26.041 -4.546 0.645 3.140 17.435 2.595 27.277 8 DD_DT19DA20:DT2DA3_EE D 19 ? E 3 ? D 20 ? E 2 ? 1 A DA 9 1_555 B DT 2 1_555 A DG 10 1_555 B DC 1 1_555 0.782 -0.105 3.112 -0.750 -1.602 39.560 0.023 -1.238 3.099 -2.366 1.107 39.598 9 DD_DA20DG21:DC1DT2_EE D 20 ? E 2 ? D 21 ? E 1 ? # _pdbx_entity_nonpoly.entity_id 4 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #